News
Youtube: Mascot Server 3.0
Overview of new features and improvements in Mascot Server 3.0 is now available on our Youtube channel!
Mascot Server 3.0 is now running at matrixscience.com
The free Mascot service running on this website has now been updated to version 3.0.
What’s new in Mascot Server 3.0
If something isn’t working, please check the known issues in version 3.0 or contact us by e-mail.
Mascot Server 3.0 has been released
We are pleased to announce the official release of Mascot Server 3.0.
What’s new in Mascot Server 3.0
Customers with an active support contract receive the new version for free. If you’d like to update an earlier version, please contact us by e-mail or send us a quote request.
Mascot Server 3.0 release candidate
This website is now running a Mascot Server 3.0 release candidate, which is undergoing extensive beta testing.
What’s new in Mascot Server 3.0
If you spot any bugs or experience any problems, please email support@matrixscience.com with details. No matter how much testing we do ourselves, there will always be some bugs that we miss.
New Mascot distributor in Europe: MS Wil B.V.
We are pleased to announce a new distributor for Matrix Science products!
Customers in Europe can now buy Mascot through MS Wil B.V., a one-stop-shop for fine mass spectrometry tools. MS Wil is selling new licences for Mascot Server and Mascot Distiller as well as updates and upgrades to existing licences.
The new distribution agreement means buying Mascot has never been easier: specify Mascot as part of your instrument package when buying through Bruker, Shimadzu, Thermo or Waters; order from MS Wil when stocking up on lab consumables; or buy direct from Matrix Science Ltd.
If you have an existing support contract, there is no change to your support status. Licences bought through European distributors and marketing partners continue to supported directly by Mascot developers based in the UK.
Obsolete IPI definitions and SARS-CoV-2 pre-release definition have been removed
Mascot Server ships with predefined configuration for several sequence databases, stored in databases_1.xml. The following definitions have become obsolete and have now been removed from databases_1.xml:
- IPI_arabidopsis
- IPI_bovine
- IPI_chicken
- IPI_human
- IPI_mouse
- IPI_rat
- IPI_zebrafish
- SARS-CoV-2
The International Protein Index (IPI) databases were superceded by Uniprot proteomes as long ago as September 2011. We kept the predefined definitions, because the FASTA files were still available at the EBI website. However, those files are no longer available, so there is no reason to keep these long-obsoleted definitions.
The SARS-CoV-2 predefined definition was added in March 2020, when Uniprot published a pre-release database for the virus. Since then, the sequences have been reviewed and incorporated in SwissProt, and in fact, the pre-release FASTA file disappeared from the Uniprot servers around September 2023. There is no reason to keep the SARS-CoV-2 definition – please use SwissProt instead, or set up a suitable Uniprot proteome database.
Removing the predefined definitions does not delete any databases in your local Mascot Server installation. If you had enabled any of the above, their local configuration points to the previous version of databases_1.xml and the sequence databases continue to work. The removal simply means you won’t be able to enable them on a new system or re-enable if you delete them. If you still need the databases, it’s best to make a copy in Database Manager and make sure it’s part of your backups.
Server upgrade
We have upgraded the server hardware and operating system, as well as migrated to a new hosting provider. The website and the free Mascot service should now operate normally. If you discover any issues, please contact us at support@matrixscience.com.
We have additionally moved searches older than 1 Jan 2020 to cold storage. If you submitted a search before 1 Jan 2020 and would like to download a copy, please send us an e-mail and we can send you the results file.
The server migration was originally scheduled for Saturday 20 January, with expected maximum downtime of 6 hours. The old server was meant to be running until the morning of 20 January, then switch over to the new server.
At about 16:15 UTC on Tuesday 16 January, we were finalising data migration and setting up the new server when the network connection to the old server was abruptly lost. Our previous hosting provider disconnected the IP feed without telling us. Because they could not provide any time estimate for restoring the IP feed, we accelerated the migration schedule to Wednesday 17 January. We apologise for the unplanned and extended downtime, which was due to actions outside our control.
If you submitted Mascot searches between 14 January 23:00 UTC and 16 January 16:15 UTC, your search results have not yet been copied to the new server. UPDATED on 18 Jan: We have now copied the 14-16 January searches to the new server. No data has been lost. Please e-mail us if you have any questions.
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